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Volumn 7, Issue 8, 2008, Pages 3373-3381

Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis

Author keywords

High throughput proteomics; Phosphoproteomics; Post translational modifications; Scoring

Indexed keywords

ARTICLE; COMPUTER PROGRAM; MASS SPECTROMETRY; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SCORING SYSTEM; ALGORITHM; BAYES THEOREM; CHEMISTRY; PHOSPHORYLATION; PROBABILITY; SCHIZOSACCHAROMYCES; STATISTICAL MODEL; TANDEM MASS SPECTROMETRY;

EID: 53049084796     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800129m     Document Type: Article
Times cited : (51)

References (34)
  • 1
    • 33745800293 scopus 로고    scopus 로고
    • Interpreting the protein language using proteomics
    • Jensen, O. N. Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell. Biol. 2006, 7, 391-403.
    • (2006) Nat. Rev. Mol. Cell. Biol , vol.7 , pp. 391-403
    • Jensen, O.N.1
  • 2
    • 0034614490 scopus 로고    scopus 로고
    • Signaling-2000 and beyond
    • Hunter, T. Signaling-2000 and beyond. Cell 2000, 100, 113-127.
    • (2000) Cell , vol.100 , pp. 113-127
    • Hunter, T.1
  • 3
    • 0035072715 scopus 로고    scopus 로고
    • A systematic approach to the analysis of protein phosphorylation
    • Zhou, H.; Watts, J. D.; Aebersold, R. A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 2001, 19, 375-378.
    • (2001) Nat. Biotechnol , vol.19 , pp. 375-378
    • Zhou, H.1    Watts, J.D.2    Aebersold, R.3
  • 4
    • 0022541790 scopus 로고
    • Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography
    • Andersson, L.; Porath, J. Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. Anal. Biochem. 1986, 154, 250-254.
    • (1986) Anal. Biochem , vol.154 , pp. 250-254
    • Andersson, L.1    Porath, J.2
  • 5
    • 3242688830 scopus 로고    scopus 로고
    • Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns
    • Pinkse, M. W. H.; Uitto, P. M.; Hilhorst, M. J.; Ooms, B.; Heck, A. J. R. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem. 2004, 76, 3935-3943.
    • (2004) Anal. Chem , vol.76 , pp. 3935-3943
    • Pinkse, M.W.H.1    Uitto, P.M.2    Hilhorst, M.J.3    Ooms, B.4    Heck, A.J.R.5
  • 8
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648.
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4    Kumar, C.5    Mortensen, P.6    Mann, M.7
  • 10
    • 33847782587 scopus 로고    scopus 로고
    • Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry
    • Molina, H.; Horn, D. M.; Tang, N.; Mathivanan, S.; Pandey, A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. U.SA. 2007, 104, 2199-2204.
    • (2007) Proc. Natl. Acad. Sci. U.SA , vol.104 , pp. 2199-2204
    • Molina, H.1    Horn, D.M.2    Tang, N.3    Mathivanan, S.4    Pandey, A.5
  • 11
    • 34248640306 scopus 로고    scopus 로고
    • Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis
    • Chitted, B. R.; Peng, Z. Proteome and phosphoproteome dynamic change during cell dedifferentiation in Arabidopsis. Proteomics 2007, 7, 1473-1500.
    • (2007) Proteomics , vol.7 , pp. 1473-1500
    • Chitted, B.R.1    Peng, Z.2
  • 12
    • 2642521977 scopus 로고    scopus 로고
    • Identification of phosphoproteins and their phosphorylation sites in the WEHI-231 B lymphoma cell line
    • Shu, H.; Chen, S.; Bi, Q.; Mumby, M.; Brekken, D. L. Identification of phosphoproteins and their phosphorylation sites in the WEHI-231 B lymphoma cell line. Mol. Cell. Proteomics 2004, 3, 279-286.
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 279-286
    • Shu, H.1    Chen, S.2    Bi, Q.3    Mumby, M.4    Brekken, D.L.5
  • 15
    • 34247383227 scopus 로고    scopus 로고
    • Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS
    • Lee, J.; Xu, Y.; Chen, Y.; Sprung, R.; Kim, S. C.; Xie, S.; Zhao, Y. Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS. Mol. Cell. Proteomics 2007, 6, 669-676.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 669-676
    • Lee, J.1    Xu, Y.2    Chen, Y.3    Sprung, R.4    Kim, S.C.5    Xie, S.6    Zhao, Y.7
  • 16
    • 0032237775 scopus 로고    scopus 로고
    • Fragmentation of phosphopeptides in an ion trap mass spectrometer
    • DeGnore, J. P.; Qin, J. Fragmentation of phosphopeptides in an ion trap mass spectrometer. J Am. Soc. Mass Spectrom. 1998, 9, 1175-1188.
    • (1998) J Am. Soc. Mass Spectrom , vol.9 , pp. 1175-1188
    • DeGnore, J.P.1    Qin, J.2
  • 17
    • 33749853607 scopus 로고    scopus 로고
    • A probability-based approach for high- throughput protein phosphorylation analysis and site localization
    • Beausoleil, S. A.; Villen, J.; Gerber, S. A.; Rush, J.; Gygi, S. P. A probability-based approach for high- throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 2006, 24, 1285-1292.
    • (2006) Nat. Biotechnol , vol.24 , pp. 1285-1292
    • Beausoleil, S.A.1    Villen, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 18
    • 33847194634 scopus 로고    scopus 로고
    • Automatic validation of phosphopeptide identifications from tandem mass spectra
    • Lu, B.; Ruse, C.; Xu, T.; Park, S. K.; 3rd Yates, J. Automatic validation of phosphopeptide identifications from tandem mass spectra. Anal. Chem. 2007, 79, 1301-1310.
    • (2007) Anal. Chem , vol.79 , pp. 1301-1310
    • Lu, B.1    Ruse, C.2    Xu, T.3    Park 3rd, S.K.4    Yates, J.5
  • 19
    • 0027461675 scopus 로고
    • 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization
    • Loo, J. A.; Edmonds, C. G.; Smith, R. D. 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization. Anal. Chem. 1993, 65, 425-438.
    • (1993) Anal. Chem , vol.65 , pp. 425-438
    • Loo, J.A.1    Edmonds, C.G.2    Smith, R.D.3
  • 21
    • 0037317111 scopus 로고    scopus 로고
    • Intensity-based statistical scorer for tandem mass spectrometry
    • Havilio, M.; Haddad, Y.; Smilansky, Z. Intensity-based statistical scorer for tandem mass spectrometry. Anal. Chem. 2003, 75, 435-444.
    • (2003) Anal. Chem , vol.75 , pp. 435-444
    • Havilio, M.1    Haddad, Y.2    Smilansky, Z.3
  • 24
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
    • Tanner, S.; Shu, H.; Frank, A.; Wang, L.; Zandi, E.; Mumby, M.; Pevzner, P. A.; Bafna, V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 2005, 77, 4626-4639.
    • (2005) Anal. Chem , vol.77 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 25
    • 34547499407 scopus 로고    scopus 로고
    • Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases
    • Smolka, M. B.; Albuquerque, C. P.; Chen, S.; Zhou, H. Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc. Natl. Acad. Sci. U.SA. 2007, 104, 10364-10369.
    • (2007) Proc. Natl. Acad. Sci. U.SA , vol.104 , pp. 10364-10369
    • Smolka, M.B.1    Albuquerque, C.P.2    Chen, S.3    Zhou, H.4
  • 26
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass-spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K.; McCormack, A. L.; Yates, J. R. An approach to correlate tandem mass-spectral data of peptides with amino acid sequences in a protein database. J Am. Soc. Mass Spectrom. 1994, 5, 976-989.
    • (1994) J Am. Soc. Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 28
    • 33645235084 scopus 로고    scopus 로고
    • Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra
    • Venable, J. D.; Xu, T.; Cociorva, D.; Yates, J. R., III. Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra. Anal. Chem. 2006, 78, 1921-1929.
    • (2006) Anal. Chem , vol.78 , pp. 1921-1929
    • Venable, J.D.1    Xu, T.2    Cociorva, D.3    Yates III, J.R.4
  • 30
    • 33845703344 scopus 로고    scopus 로고
    • What is a support vector machine
    • Noble, W. S. What is a support vector machine. Nat. Biotechnol. 2006, 24, 1565-1567.
    • (2006) Nat. Biotechnol , vol.24 , pp. 1565-1567
    • Noble, W.S.1
  • 32
    • 33746930864 scopus 로고    scopus 로고
    • A uniform proteomics MS/MS analysis platform utilizing open XML file formats
    • Keller, A.; Eng, J.; Zhang, N.; Li, X.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1, 2005-0017.
    • (2005) Mol. Syst. Biol , vol.1 , pp. 2005-0017
    • Keller, A.1    Eng, J.2    Zhang, N.3    Li, X.4    Aebersold, R.5
  • 33
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 34
    • 24044513966 scopus 로고    scopus 로고
    • Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
    • Elias, J. E.; Haas, W.; Faherty, B. K.; Gygi, S. P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2005, 2, 667-675.
    • (2005) Nat. Methods , vol.2 , pp. 667-675
    • Elias, J.E.1    Haas, W.2    Faherty, B.K.3    Gygi, S.P.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.